Control of Leaf Senescence by an MeOH-Jasmonates Cascade that Is Epigenetically Regulated by OsSRT1 in Rice

AtSRT1 regulates flowering by regulating flowering integrators and energy signals in Arabidopsis

Epigenetic modifications, such as histone alterations, play crucial roles in regulating the flowering process in Arabidopsis, a typical long-day model plant. Histone modifications are notably involved in the intricate regulation of FLC, a key inhibitor of flowering. Although sirtuin-like protein and NAD+-dependent deacetylases play an important role in regulating energy metabolism, plant stress responses, and hormonal signal transduction, the mechanisms underlying their developmental transitions remain unclear. Thus, this study aimed to reveal how Arabidopsis NAD + -dependent deacetylase AtSRT1 affects flowering by regulating the expression of flowering integrators. Genetic and molecular evidence demonstrated that AtSRT1 mediates histone deacetylation by directly binding near the transcriptional start sites (TSS) of the flowering integrator genes FT and SOC1 and negatively regulating their expression by modulating the expression of the downstream gene LFY to inhibit flowering. Additionally, AtSRT1 directly down-regulates the expression of TOR, a glucose-driven central hub of energy signaling, which controls cell metabolism and growth in response to nutritional and environmental factors. This down-regulation occurs through binding near the TSS of TOR, facilitating the addition of H3K27me3 marks on FLC via the TOR-FIE-PRC2 pathway, further repressing flowering. These results uncover a multi-pathway regulatory network involving deacetylase AtSRT1 during the flowering process, highlighting its interaction with TOR as a hub for the coordinated regulation of energy metabolism and flowering initiation. These findings significantly enhance understanding of the complexity of histone modifications in the regulation of flowering.

Epigenetic control of plant senescence and cell death and its application in crop improvement

Plant senescence is the last stage of plant development and a type of programmed cell death, occurring at a predictable time and cell. It involves the functional conversion from nutrient assimilation to nutrient remobilization, which substantially impacts plant architecture and plant biomass, crop quality, and horticultural ornamental traits. In past two decades, DNA damage was believed to be a main reason for cell senescence. Increasing evidence suggests that the alteration of epigenetic information is a contributing factor to cell senescence in organisms. In this review, we summarize the current research progresses of epigenetic and epitranscriptional mechanism involved in cell senescence of plant, at the regulatory level of DNA methylation, histone methylation and acetylation, chromatin remodeling, non-coding RNAs and RNA methylation. Furthermore, we discuss their molecular genetic manipulation and potential application in agriculture for crop improvement. Finally we point out the prospects of future research topics.

Lack of the CCT domain changes the ability of mango MiCOL14A to resist salt and drought stress in Arabidopsis

CONSTANS (CO) is the key gene in the photoperiodic pathway that regulates flowering in plants. In this paper, a CONSTANS-like 14A (COL14A) gene was obtained from mango, and its expression patterns and functions were characterized. Sequence analysis shows that MiCOL14A-JH has an additional A base, which leads to code shifting in subsequent coding boxes and loss of the CCT domain. The MiCOL14A-JH and MiCOL14A-GQ genes both belonged to group Ⅲ of the CO/COL gene family. Analysis of tissue expression patterns showed that MiCOL14A was expressed in all tissues, with the highest expression in the leaves of seedling, followed by lower expression levels in the flowers and stems of adult leaves. However, there was no significant difference between different mango varieties. At different development stages of flowering, the expression level of MiCOL14A-GQ was the highest in the leaves before floral induction period, and the lowest at flowering stage, while the highest expression level of MiCOL14A-JH appeared in the leaves at flowering stage. The transgenic functional analysis showed that both MiCOL14A-GQ and MiCOL14A-JH induced delayed flowering of transgenic Arabidopsis. In addition, MiCOL14A-JH enhanced the resistance of transgenic Arabidopsis to drought stress, while MiCOL14A-GQ increased the sensitivity of transgenic Arabidopsis to salt stress. Further proteinprotein interaction analysis showed that MiCOL14A-JH directly interacted with MYB30-INTERACTING E3 LIGASE 1 (MiMIEL1), CBL-interacting protein kinase 9 (MiCIPK9) and zinc-finger protein 4 (MiZFP4), but MiCOL14A-GQ could not interact with these three stress-related proteins. Together, our results demonstrated that MiCOL14A-JH and MiCOL14A-GQ not only regulate flowering but also play a role in the abiotic stress response in mango, and the lack of the CCT domain affects the proteinprotein interaction, thus affecting the gene response to stress. The insertion of an A base can provide a possible detection site for mango resistance breeding.

Jasmonate signaling controls negative and positive effectors of salt stress tolerance in rice

Plant responses to salt exposure involve large reconfigurations of hormonal pathways that orchestrate physiological changes towards tolerance. Jasmonate (JA) hormones are essential to withstand biotic and abiotic assaults, but their roles in salt tolerance remain unclear. Here we describe the dynamics of JA metabolism and signaling in root and leaf tissue of rice, a plant species that is highly exposed and sensitive to salt. Roots activate the JA pathway in an early pulse, while the second leaf displays a biphasic JA response with peaks at 1 h and 3 d post-exposure. Based on higher salt tolerance of a rice JA-deficient mutant (aoc), we examined, through kinetic transcriptome and physiological analysis, the salt-triggered processes that are under JA control. Profound genotype-differential features emerged that could underlie the observed phenotypes. Abscisic acid (ABA) content and ABA-dependent water deprivation responses were impaired in aoc shoots. Moreover, aoc accumulated more Na+ in roots, and less in leaves, with reduced ion translocation correlating with root derepression of the HAK4 Na+ transporter gene. Distinct reactive oxygen species scavengers were also stronger in aoc leaves, along with reduced senescence and chlorophyll catabolism markers. Collectively, our results identify contrasted contributions of JA signaling to different sectors of the salt stress response in rice.

Transmembrane potential, an indicator in situ reporting cellular senescence and stress response in plant tissues

BACKGROUND

Plant cells usually sustain a stable membrane potential due to influx and/or efflux of charged ions across plasma membrane. With the growth and development of plants, different tissues and cells undergo systemic or local programmed decline. Whether the membrane potential of plasma membrane could report senescence signal of plant tissues and cells is unclear.

RESULTS

We applied a maneuverable transmembrane potential (TMP) detection method with patch-clamp setup to examine the senescence signal of leaf tissue cells in situ over the whole life cycle in Arabidopsis thaliana. The data showed that the TMPs of plant tissues and cells were varied at different growth stages, and the change of TMP was higher at the vegetative growth stage than at the reproductive stage of plant growth. The distinct change of TMP was detectable between the normal and the senescent tissues and cells in several plant species. Moreover, diverse abiotic stimuli, such as heat stress, hyperpolarized the TMP in a short time, followed by depolarized membrane potential with the senescence occurring. We further examined the TMP of plant chloroplasts, which also indicates the senescence signal in organelles.

CONCLUSIONS

This convenient TMP detection method can report the senescence signal of plant tissues and cells, and can also indicate the potential of plant tolerance to environmental stress.

Fine mapping and cloning of a novel BrSCC1 gene for seed coat color in Brassica rapa L

A novel BrSCC1 gene for seed coat color was fine mapped within a 41.1-kb interval on chromosome A03 in Brassica rapa and functionally validated by ectopic expression analysis. Yellow seed is a valuable breeding trait that can be potentiality applied for improving seed quality and oil productivity in oilseed Brassica crops. However, only few genes for yellow seed have been identified in B. rapa. We previously identified a minor quantitative trait locus (QTL), qSC3.1, for seed coat color on chromosome A03 in B. rapa. In order to isolate the seed coat color gene, a brown-seeded chromosome segment substitution line, CSSL-38, harboring the qSC3.1, was selected and crossed with the yellow-seeded recurrent parent, a rapid cycling inbred line of B. rapa (RcBr), to construct the secondary F₂ population. Metabolite identification suggested that seed coat coloration in CSSL-38 was independent of proanthocyanidins (PAs) accumulation. Genetic analysis revealed that yellow seed was controlled by a single recessive gene, Seed Coat Color 1 (BrSCC1). Utilizing bulked segregant analysis (BSA)-seq and secondary F₂ and F_2:3 recombinants analysis, BrSCC1 was fine mapped within a 41.1-kb interval. By integrating gene expression profiling, genome sequence comparison, metabolite analysis, and functional validation through ectopic expression in Arabidopsis, the BraA03g040800.3C gene was confirmed to be BrSCC1, which positively correlated with the seed coat coloration. Our study provides a novel gene resource for the genetic improvement of yellow seeds in oilseed B. rapa.

Regulation of floral senescence in Arabidopsis by coordinated action of CONSTANS and jasmonate signaling

In Arabidopsis, photoperiodic flowering is controlled by the regulatory hub gene CONSTANS (CO), whereas floral organ senescence is regulated by the jasmonates (JAs). Because these processes are chronologically ordered, it remains unknown whether there are common regulators of both processes. In this study, we discovered that CO protein accumulates in Arabidopsis flowers after floral induction, and it displays a diurnal pattern in floral organs different from that in the leaves. We observed that altered CO expression could affect flower senescence and abscission by interfering with JA response, as shown by petal-specific transcriptomic analysis as well as CO overexpression in JA synthesis and signaling mutants. We found that CO has a ZIM (ZINC-FINGER INFLORESCENCE MERISTEM) like domain that mediates its interaction with the JA response repressor JAZ3 (jasmonate ZIM-domain 3). Their interaction inhibits the repressor activity of JAZ3, resulting in activation of downstream transcription factors involved in promoting flower senescence. Furthermore, we showed that CO, JAZ3, and the E3 ubiquitin ligase COI1 (Coronatine Insensitive 1) could form a protein complex in planta, which promotes the degradation of both CO and JAZ3 in the presence of JAs. Taken together, our results indicate that CO, a key regulator of photoperiodic flowering, is also involved in promoting flower senescence and abscission by augmenting JA signaling and response. We propose that coordinated recruitment of photoperiodic and JA signaling pathways could be an efficient way for plants to chronologically order floral processes and ensure the success of offspring production.

Genome-wide association studies of five free amino acid levels in rice

Rice (Oryza sativa L.) is one of the important staple foods for human consumption and livestock use. As a complex quality trait, free amino acid (FAA) content in rice is of nutritional importance. To dissect the genetic mechanism of FAA level, five amino acids' (Val, Leu, Ile, Arg, and Trp) content and 4,325,832 high-quality SNPs of 448 rice accessions were used to conduct genome-wide association studies (GWAS) with nine different methods. Of these methods, one single-locus method (GEMMA), seven multi-locus methods (mrMLM, pLARmEB, FASTmrEMMA, pKWmEB, FASTmrMLM, ISIS EM-BLASSO, and FarmCPU), and the recent released 3VmrMLM were adopted for methodological comparison of quantitative trait nucleotide (QTN) detection and identification of stable quantitative trait nucleotide loci (QTLs). As a result, 987 QTNs were identified by eight multi-locus GWAS methods; FASTmrEMMA detected the most QTNs (245), followed by 3VmrMLM (160), and GEMMA detected the least QTNs (0). Among 88 stable QTLs identified by the above methods, 3VmrMLM has some advantages, such as the most common QTNs, the highest LOD score, and the highest proportion of all detected stable QTLs. Around these stable QTLs, candidate genes were found in the GO classification to be involved in the primary metabolic process, biosynthetic process, and catalytic activity, and shown in KEGG analysis to have participated in metabolic pathways, biosynthesis of amino acids, and tryptophan metabolism. Natural variations of candidate genes resulting in the content alteration of five FAAs were identified in this association panel. In addition, 95 QTN-by-environment interactions (QEIs) of five FAA levels were detected by 3VmrMLM only. GO classification showed that the candidate genes got involved in the primary metabolic process, transport, and catalytic activity. Candidate genes of QEIs played important roles in valine, leucine, and isoleucine degradation (QEI_09_03978551 and candidate gene LOC_Os09g07830 in the Leu dataset), tryptophan metabolism (QEI_01_00617184 and candidate gene LOC_Os01g02020 in the Trp dataset), and glutathione metabolism (QEI_12_09153839 and candidate gene LOC_Os12g16200 in the Arg dataset) pathways through KEGG analysis. As an alternative of the multi-locus GWAS method, these findings suggested that the application of 3VmrMLM may provide new insights into better understanding FAA accumulation and facilitate the molecular breeding of rice with high FAA level.

Understanding the catalytic abilities of class IV sirtuin OsSRT1 and its linkage to the DNA repair system under stress conditions

The roles of sirtuins in plants are slowly unraveling. Regarding OsSRT1, there are only reports of its H3K9Ac deacetylation. Here we detect the other lysine deacetylation sites in histones, H3 and H4. Further, our studies shed light on its dual enzyme capability with preference for mono ADP ribosylation over deacetylation. OsSRT1 can specifically transfer the single ADP ribose group on its substrates in an enzymatic manner. This mono ADPr effect is not well known in plants, more so for deacetylases. The products of this reaction (NAM and ADP ribose) have a negative effect on this enzyme's action suggesting a tighter regulation. Resveratrol, a natural plant polyphenol proves to be a good activator of this enzyme at 150 ± 40 µM concentration. Under different abiotic stress conditions, we could link this ADP ribosylase activity to the DNA damage repair (DDR) pathway by activating the enzyme PARP1. There is also evidence of OsSRT1's interaction with the components of DDR machinery. Changes in the extent of different histone deacetylation by OsSRT1 is also related with these stress conditions. Metal stress in plants also influences these enzyme activities. Structurally there is a long C-terminal domain in OsSRT1 in comparison to other classes of plant sirtuins, which is required for its catalysis.

Genome-wide H3K9 acetylation level increases with age-dependent senescence of flag leaf in rice

Flag leaf senescence is an important biological process that drives the remobilization of nutrients to the growing organs of rice. Leaf senescence is controlled by genetic information via gene expression and histone modification, but the precise mechanism is as yet unclear. Here, we analysed genome-wide acetylated lysine residue 9 of histone H3 (H3K9ac) enrichment by chromatin immunoprecipitation-sequencing (ChIP-seq), and examined its association with transcriptomes by RNA-seq during flag leaf aging in rice (Oryza sativa). We found that genome-wide H3K9 acetylation levels increased with age-dependent senescence in rice flag leaf, and there was a positive correlation between the density and breadth of H3K9ac with gene expression and transcript elongation. During flag leaf aging, we observed 1249 up-regulated differentially expressed genes (DEGs) and 996 down-regulated DEGs, showing a strong relationship between temporal changes in gene expression and gain/loss of H3K9ac. We produced a landscape of H3K9 acetylation-modified gene expression targets that include known senescence-associated genes, metabolism-related genes, as well as miRNA biosynthesis-related genes. Our findings reveal a complex regulatory network of metabolism- and senescence-related pathways mediated by H3K9ac, and elucidate patterns of H3K9ac-mediated regulation of gene expression during flag leaf aging in rice.

Reprogramming rice leaves: another layer of senescence regulation

This article comments on:

Zhang Y, Li Y, Zhang Y, Zhang Z, Zhang D, Wang X, Lai B, Huang D, Gu L, Xie Y, Miao Y. 2022. Genome-wide H3K9 acetylation level increases with age-dependent senescence of flag leaf in rice (Oryza sativa). Journal of Experimental Botany 73,4696–4715.

Metabolic Response to Tick-Borne Encephalitis Virus Infection and Bacterial Co-Infections

Ticks are vectors of various pathogens, including tick-borne encephalitis virus and bacteria such as B. burgdorferi and A. phagocytophilum, causing infections/co-infections, which are still a diagnostic and therapeutic problem. Therefore, the aim of this study was to compare the effects of TBEV infection/bacterial co-infection on metabolic changes in the blood of patients before and after treatment. It was found that those infections promote plasma ROS enhanced generation and antioxidant defence reduction, especially in relation to glutathione and thioredoxin systems, despite the increased effectiveness of Nrf2 transcription factor in granulocytes. Observed oxidative stress promotes the oxidative modifications of phospholipids containing polyunsaturated fatty acids (LA, AA, EPA) with increased lipid peroxidation (estimated as 8-isoPGF2α, 4-HNE). It is accompanied by protein modifications measured as 4-HNE-protein adducts, carbonyl groups, dityrosine increase, and tryptophan level decrease, which promote structural and functional modification of the following transcription factors: Nrf2 and NFkB inhibitors. The lower level of 8-iso-PGF2α in co-infections indicates an impairment of the body’s ability to intensify inflammation and fight co-infections, while an increased level of Trx after therapy may contribute to the intensification of the inflammatory process. The obtained results indicate the potential possibility of using the assessed metabolic parameters to introduce targeted pharmacotherapy in cases of TBEV infections/bacterial co-infections.

How salt stress-responsive proteins regulate plant adaptation to saline conditions

An overview is presented of recent advances in our knowledge of candidate proteins that regulate various physiological and biochemical processes underpinning plant adaptation to saline conditions. Salt stress is one of the environmental constraints that restrict plant distribution, growth and yield in many parts of the world. Increased world population surely elevates food demands all over the globe, which anticipates to add a great challenge to humanity. These concerns have necessitated the scientists to understand and unmask the puzzle of plant salt tolerance mechanisms in order to utilize various strategies to develop salt tolerant crop plants. Salt tolerance is a complex trait involving alterations in physiological, biochemical, and molecular processes. These alterations are a result of genomic and proteomic complement readjustments that lead to tolerance mechanisms. Proteomics is a crucial molecular tool that indicates proteins expressed by the genome, and also identifies the functions of proteins accumulated in response to salt stress. Recently, proteomic studies have shed more light on a range of promising candidate proteins that regulate various processes rendering salt tolerance to plants. These proteins have been shown to be involved in photosynthesis and energy metabolism, ion homeostasis, gene transcription and protein biosynthesis, compatible solute production, hormone modulation, cell wall structure modification, cellular detoxification, membrane stabilization, and signal transduction. These candidate salt responsive proteins can be therefore used in biotechnological approaches to improve tolerance of crop plants to salt conditions. In this review, we provided comprehensive updated information on the proteomic data of plants/genotypes contrasting in salt tolerance in response to salt stress. The roles of salt responsive proteins that are potential determinants for plant salt adaptation are discussed. The relationship between changes in proteome composition and abundance, and alterations observed in physiological and biochemical features associated with salt tolerance are also addressed.

OsRLCK160 contributes to flavonoid accumulation and UV-B tolerance by regulating OsbZIP48 in rice

Plants produce specialized metabolites to adapt to the ever-changing environments. Flavonoids are antioxidants essential for growth, development, and breeding with increased stress resistance in crops. However, the mechanism of the involvement of flavonoids in ultraviolet-B (UV-B) stress in rice (Oryza sativa) is largely unknown. In this study, we cloned and functionally identified a receptor-like kinase (OsRLCK160) and a bZIP transcription factor (OsbZIP48) positively regulating flavonoid accumulation through metabolite-based genome-wide association study of the flavonoid content in rice. Meanwhile, OsRLCK160 interacted with and phosphorylated OsbZIP48 to regulate the flavonoid accumulation and participate in UV-B tolerance in rice. Our study indicates the importance of applying OsRLCK160 and OsbZIP48 to advance the fundamental understanding of stable rice production and breed UV-B-tolerant rice varieties, which may contribute to breeding high-yield rice varieties.

Structural and functional insights into the candidate genes associated with different developmental stages of flag leaf in bread wheat (Triticum aestivum L.)

Grain yield is one of the most important aims for combating the needs of the growing world population. The role of development and nutrient transfer in flag leaf for higher yields at the grain level is well known. It is a great challenge to properly exploit this knowledge because all the processes, starting from the emergence of the flag leaf to the grain filling stages of wheat (Triticum aestivum L.), are very complex biochemical and physiological processes to address. This study was conducted with the primary goal of functionally and structurally annotating the candidate genes associated with different developmental stages of flag leaf in a comprehensive manner using a plethora of in silico tools. Flag leaf-associated genes were analyzed for their structural and functional impacts using a set of bioinformatics tools and algorithms. The results revealed the association of 17 candidate genes with different stages of flag leaf development in wheat crop. Of these 17 candidate genes, the expression analysis results revealed the upregulation of genes such as TaSRT1-5D, TaPNH1-7B, and TaNfl1-2B and the downregulation of genes such as TaNAP1-7B, TaNOL-4D, and TaOsl2-2B can be utilized for the generation of high-yielding wheat varieties. Through MD simulation and other in silico analyses, all these proteins were found to be stable. Based on the outcome of bioinformatics and molecular analysis, the identified candidate genes were found to play principal roles in the flag leaf development process and can be utilized for higher-yield wheat production.

Therapeutic Potential of Jasmonic Acid and Its Derivatives

A modern method of therapeutic use of natural compounds that would protect the body are jasmonates. The main representatives of jasmonate compounds include jasmonic acid and its derivatives, mainly methyl jasmonate. Extracts from plants rich in jasmonic compounds show a broad spectrum of activity, i.e., anti-cancer, anti-inflammatory and cosmetic. Studies of the biological activity of jasmonic acid and its derivatives in mammals are based on their structural similarity to prostaglandins and the compounds can be used as natural therapeutics for inflammation. Jasmonates also constitute a potential group of anti-cancer drugs that can be used alone or in combination with other known chemotherapeutic agents. Moreover, due to their ability to stimulate exfoliation of the epidermis, remove discoloration, regulate the function of the sebaceous glands and reduce the visible signs of aging, they are considered for possible use in cosmetics and dermatology. The paper presents a review of literature data on the biological activity of jasmonates that may be helpful in treatment and prevention.

Comparative analysis of tuberous root metabolites between cultivated and wild varieties of Rehmannia glutinosa by widely targeted metabolomics

Differential metabolites between tuberous roots from cultivated variety (ZP) and wild variety (YS) of Rehmannia glutinosa were analyzed by widely targeted metabolomics, and annotated to KEGG pathways. 228 secondary metabolites (SM) in ZP and YS were detected, of which 58 were differential metabolites (DM), including 41 flavonoids, 10 phenolic acids, 3 terpenoids, 2 alkaloids and 2 others, and 170 were unchanged; Among 58 DMs, 44 (75.9%) were up-regulated in YS, of which 30 were unique to YS, while 14 (24.1%) were down-regulated in YS, of which 10 were unique to ZP; Among flavonoids, 33 (80.5%) were more highly expressed in YS than in ZP; Among phenolic acids, 7 (70%) were more highly expressed in YS than in ZP; 12 of 58 DMs were annotated into 17 types of KEGG pathways. Among them, benzoic acid and p-Coumaryl alcohol were up-regulated in YS, and annotated into 10 pathways (58.8%) and 4 pathways (23.5%), respectively. In addition, much of DMs possess various pharmacological effects. These results indicated better quality of YS than ZP and the necessity of YS domestication. Taken together, this study will provide a reference for the scientific introduction, comprehensive development and utilization of wild Rehmannia glutinosa.

Genome-wide identification and characterization of long non-coding RNAs involved in flag leaf senescence of rice

KEY MESSAGE

This study showed the systematic identification of long non-coding RNAs (lncRNAs) involving in flag leaf senescence of rice, providing the possible lncRNA-mRNA regulatory relationships and lncRNA-miRNA-mRNA ceRNA networks during leaf senescence. LncRNAs have been reported to play crucial roles in diverse biological processes. However, no systematic identification of lncRNAs associated with leaf senescence in plants has been studied. In this study, a genome-wide high throughput sequencing analysis was performed using rice flag leaves developing from normal to senescence. A total of 3953 lncRNAs and 38757 mRNAs were identified, of which 343 lncRNAs and 9412 mRNAs were differentially expressed. Through weighted gene co-expression network analysis (WGCNA), 22 continuously down-expressed lncRNAs targeting 812 co-expressed mRNAs and 48 continuously up-expressed lncRNAs targeting 1209 co-expressed mRNAs were considered to be significantly associated with flag leaf senescence. Gene Ontology results suggested that the senescence-associated lncRNAs targeted mRNAs involving in many biological processes, including transcription, hormone response, oxidation-reduction process and substance metabolism. Additionally, 43 senescence-associated lncRNAs were predicted to target 111 co-expressed transcription factors. Interestingly, 8 down-expressed lncRNAs and 29 up-expressed lncRNAs were found to separately target 12 and 20 well-studied senescence-associated genes (SAGs). Furthermore, analysis on the competing endogenous RNA (CeRNA) network revealed that 6 down-expressed lncRNAs possibly regulated 51 co-expressed mRNAs through 15 miRNAs, and 14 up-expressed lncRNAs possibly regulated 117 co-expressed mRNAs through 21 miRNAs. Importantly, by expression validation, a conserved miR164-NAC regulatory pathway was found to be possibly involved in leaf senescence, where lncRNA MSTRG.62092.1 may serve as a ceRNA binding with miR164a and miR164e to regulate three transcription factors. And two key lncRNAs MSTRG.31014.21 and MSTRG.31014.36 also could regulate the abscisic-acid biosynthetic gene BGIOSGA025169 (OsNCED4) and BGIOSGA016313 (NAC family) through osa-miR5809. The possible regulation networks of lncRNAs involving in leaf senescence were discussed, and several candidate lncRNAs were recommended for prior transgenic analysis. These findings will extend the understanding on the regulatory roles of lncRNAs in leaf senescence, and lay a foundation for functional research on candidate lncRNAs.

Maintenance of Cell Wall Integrity under High Salinity

Cell wall biosynthesis is a complex biological process in plants. In the rapidly growing cells or in the plants that encounter a variety of environmental stresses, the compositions and the structure of cell wall can be dynamically changed. To constantly monitor cell wall status, plants have evolved cell wall integrity (CWI) maintenance system, which allows rapid cell growth and improved adaptation of plants to adverse environmental conditions without the perturbation of cell wall organization. Salt stress is one of the abiotic stresses that can severely disrupt CWI, and studies have shown that the ability of plants to sense and maintain CWI is important for salt tolerance. In this review, we highlight the roles of CWI in salt tolerance and the mechanisms underlying the maintenance of CWI under salt stress. The unsolved questions regarding the association between the CWI and salt tolerance are discussed.

Methyl jasmonate mitigates high selenium damage of rice via altering antioxidant capacity, selenium transportation and gene expression

Beneficial effects of methyl jasmonate (MeJA) on plants under different abiotic conditions have long been demonstrated. This study aimed to figure out how exogenous MeJA mitigated high-Se toxicity in rice from plant physiology and gene express perspective to provide the theory and technique for safe production of Se-rich rice. The results showed that low concentrations of MeJA at 0.1-1.0 μM inhibited high-Se induced nonreversible toxicity by enhancing antioxidant-system and reducing H₂O₂ and MDA content in rice seedlings. In comparison with control, addition of low concentrations of MeJA at 0.1-1.0 μM reduced the Se content in roots by 13.6-48.8% and in shoots by 52.6-59.9%. Besides, lower concentrations of MeJA decreased the Se(IV) transformation to SeCys and SeMet. The qRT-PCR analysis showed that application of low concentration of MeJA down-regulated the gene expression of OsNIP2;1, and OsPT2 in roots and OsNIP2;1, OsPT2, OsSBP1, and OsCS in shoots, which inhibited Se absorption. However, high concentrations of MeJA at 2.5-5.0 μM decreased antioxidant capacity and increased H₂O₂ and MDA content in rice seedlings. The results suggested that MeJA at 0.1-1.0 μM can be used to mitigate high-Se toxicity in rice production. This research augments the knowledge for future utilization of MeJA in down-regulating Se levels in crops.

Allelic variation in rice Fertilization Independent Endosperm 1 contributes to grain width under high night temperature stress

A higher minimum (night-time) temperature is considered a greater limiting factor for reduced rice yield than a similar increase in maximum (daytime) temperature. While the physiological impact of high night temperature (HNT) has been studied, the genetic and molecular basis of HNT stress response remains unexplored. We examined the phenotypic variation for mature grain size (length and width) in a diverse set of rice accessions under HNT stress. Genome-wide association analysis identified several HNT-specific loci regulating grain size as well as loci that are common for optimal and HNT stress conditions. A novel locus contributing to grain width under HNT conditions colocalized with Fie1, a component of the FIS-PRC2 complex. Our results suggest that the allelic difference controlling grain width under HNT is a result of differential transcript-level response of Fie1 in grains developing under HNT stress. We present evidence to support the role of Fie1 in grain size regulation by testing overexpression (OE) and knockout mutants under heat stress. The OE mutants were either unaltered or had a positive impact on mature grain size under HNT, while the knockouts exhibited significant grain size reduction under these conditions.

Benefiting others and self: Production of vitamins in plants

Vitamins maintain growth and development in humans, animals, and plants. Because plants serve as essential producers of vitamins, increasing the vitamin contents in plants has become a goal of crop breeding worldwide. Here, we begin with a summary of the functions of vitamins. We then review the achievements to date in elucidating the molecular mechanisms underlying how vitamins are synthesized, transported, and regulated in plants. We also stress the exploration of variation in vitamins by the use of forward genetic approaches, such as quantitative trait locus mapping and genome-wide association studies. Overall, we conclude that exploring the diversity of vitamins could provide new insights into plant metabolism and crop breeding.

A study of leaf-senescence genes in rice based on a combination of genomics, proteomics and bioinformatics

Leaf senescence is a highly complex, genetically regulated and well-ordered process with multiple layers and pathways. Delaying leaf senescence would help increase grain yields in rice. Over the past 15 years, more than 100 rice leaf-senescence genes have been cloned, greatly improving the understanding of leaf senescence in rice. Systematically elucidating the molecular mechanisms underlying leaf senescence will provide breeders with new tools/options for improving many important agronomic traits. In this study, we summarized recent reports on 125 rice leaf-senescence genes, providing an overview of the research progress in this field by analyzing the subcellular localizations, molecular functions and the relationship of them. These data showed that chlorophyll synthesis and degradation, chloroplast development, abscisic acid pathway, jasmonic acid pathway, nitrogen assimilation and ROS play an important role in regulating the leaf senescence in rice. Furthermore, we predicted and analyzed the proteins that interact with leaf-senescence proteins and achieved a more profound understanding of the molecular principles underlying the regulatory mechanisms by which leaf senescence occurs, thus providing new insights for future investigations of leaf senescence in rice.

Integrative Metabolomic and Transcriptomic Analyses Reveal Metabolic Changes and Its Molecular Basis in Rice Mutants of the Strigolactone Pathway

Plants have evolved many metabolites to meet the demands of growth and adaptation. Although strigolactones (SLs) play vital roles in controlling plant architecture, their function in regulating plant metabolism remains elusive. Here we report the integrative metabolomic and transcriptomic analyses of two rice SL mutants, d10 (a biosynthesis mutant) and d14 (a perception mutant). Both mutants displayed a series of metabolic and transcriptional alterations, especially in the lipid, flavonoid, and terpenoid pathways. Levels of several diterpenoid phytoalexins were substantially increased in d10 and d14, together with the induction of terpenoid gene cluster and the corresponding upstream transcription factor WRKY45, an established determinant of plant immunity. The fact that WRKY45 is a target of IPA1, which acted as a downstream transcription factor of SL signaling, suggests that SLs contribute to plant defense through WRKY45 and phytoalexins. Moreover, our data indicated that SLs may modulate rice metabolism through a vast number of clustered or tandemly duplicated genes. Our work revealed a central role of SLs in rice metabolism. Meanwhile, integrative analysis of the metabolome and transcriptome also suggested that SLs may contribute to metabolite-associated growth and defense.

Unraveling candidate genomic regions responsible for delayed leaf senescence in rice

Photosynthates generated after heading contributes to 60% - 80% of grain yield in rice. Delay in leaf senescence can contribute to a long grain-filling period and thereby increased yield. The objective of this study was to identify genomic region(s) responsible for delayed leaf senescence (DLS) and validate the role of underlying candidate genes in controlling target traits. 302 BC₂F₄ backcross-derived lines (BILs) developed from a cross between Swarna and Moroberekan were phenotyped for two seasons (DS2016 and WS2017) for chlorophyll content and yield parameters. KASPar-SNP assays based genotyping data with 193 SNPs of mapping population was used to identify the targeted genomic region(s). Significant positive correlation was observed between the two most important determinants of DLS traits viz., RDCF (reduced decline degree of chlorophyll content of flag leaf) and RDCS (reduced decline degree of chlorophyll content of second leaf) with plant height (PH), grain number per panicle (GPN), panicle length (PL), number of tiller (NT) and grain yield (GY). A total of 41 and 29 QTLs with phenotypic variance (PVE) ranging from 8.2 to 25.1% were detected for six DLS traits during DS2016 and WS2017, respectively. Out of these identified QTLs, 19 were considered as stable QTLs detected across seasons. 17 of the identified stable QTLs were found to be novel. In-silico analysis revealed five key genes regulating chlorophyll metabolism. Expression analysis of these genes confirmed their strong association with the senescence pattern in leaf tissue of parents as well as selected phenotypically extreme lines. The identified stable QTLs regulating DLS traits and validation of potential candidate genes provides insight into genetic basis of delayed senescence and is expected to contribute in enhancing grain yield through genomics-assisted breeding (GAB).

Metabolomics analysis and metabolite-agronomic trait associations using kernels of wheat (Triticum aestivum) recombinant inbred lines

Plants produce numerous metabolites that are important for their development and growth. However, the genetic architecture of the wheat metabolome has not been well studied. Here, utilizing a high-density genetic map, we conducted a comprehensive metabolome study via widely targeted LC-MS/MS to analyze the wheat kernel metabolism. We further combined agronomic traits and dissected the genetic relationship between metabolites and agronomic traits. In total, 1260 metabolic features were detected. Using linkage analysis, 1005 metabolic quantitative trait loci (mQTLs) were found distributed unevenly across the genome. Twenty-four candidate genes were found to modulate the levels of different metabolites, of which two were functionally annotated by in vitro analysis to be involved in the synthesis and modification of flavonoids. Combining the correlation analysis of metabolite-agronomic traits with the co-localization of methylation quantitative trait locus (mQTL) and phenotypic QTL (pQTL), genetic relationships between the metabolites and agronomic traits were uncovered. For example, a candidate was identified using correlation and co-localization analysis that may manage auxin accumulation, thereby affecting number of grains per spike (NGPS). Furthermore, metabolomics data were used to predict the performance of wheat agronomic traits, with metabolites being found that provide strong predictive power for NGPS and plant height. This study used metabolomics and association analysis to better understand the genetic basis of the wheat metabolism which will ultimately assist in wheat breeding.

Understanding epigenomics based on the rice model

The purpose of this paper provides a comprehensive overview of the recent researches on rice epigenomics, including DNA methylation, histone modifications, noncoding RNAs, and three-dimensional genomics. The challenges and perspectives for future research in rice are discussed. Rice as a model plant for epigenomic studies has much progressed current understanding of epigenetics in plants. Recent results on rice epigenome profiling and three-dimensional chromatin structure studies reveal specific features and implication in gene regulation during rice plant development and adaptation to environmental changes. Results on rice chromatin regulator functions shed light on mechanisms of establishment, recognition, and resetting of epigenomic information in plants. Cloning of several rice epialleles associated with important agronomic traits highlights importance of epigenomic variation in rice plant growth, fitness, and yield. In this review, we summarize and analyze recent advances in rice epigenomics and discuss challenges and directions for future research in the field.

Review: The plant sirtuins

The sirtuin family of intracellular enzymes are able to catalyze a unique β-nicotinamide adenine dinucleotide (β-NAD⁺)-dependent N^ε-acyl-lysine deacylation reaction on histone and non-histone protein substrates. Since 2000, the sirtuin family members have been identified in both prokaryotes and eukaryotes; tremendous accomplishments have also been achieved on the mechanistic and functional (pharmacological) understanding of the sirtuin-catalyzed deacylation reaction. Among the eukaryotic organisms, past research has been focused more on the yeast and mammalian sirtuins than on the plant sirtuins, however, the very presence of sirtuins in various plant species and the functional studies on plant sirtuins published thus far attest to the importance of this particular subfamily of eukaryotic sirtuins in regulating the growth and development of plants and their responses to biotic and abiotic stresses. In this review, an integrated and updated account will be presented on the biochemical, cellular, and functional profiles of all the plant sirtuins identified thus far. It is hoped that this article will also set a stage for expanded efforts in the identification, characterization, and functional interrogation of plant sirtuins; and the development and exploration of their chemical modulators (activators and inhibitors) in plant research and agriculture.

A simple and efficient cloning system for CRISPR/Cas9-mediated genome editing in rice

Rapidly growing genetics and bioinformatics studies provide us with an opportunity to obtain a global view of the genetic basis of traits, but also give a challenge to the function validation of candidate genes. CRISPR/Cas9 is an emerging and efficient tool for genome editing. To construct expression clones for the CRISPR/Cas9, most current methods depend on traditional cloning using Gateway reaction or specific type IIS restriction enzymes and DNA ligation, based on multiple steps of PCR. We developed a system for introducing sgRNA expression cassette(s) directly into plant binary vectors in one step. In this system, one sgRNA expression cassette(s) is generated by an optimized multiplex PCR, in which an overlapping PCR took place. Whilst, two sgRNA expression cassettes were amplified in a single round of PCR. Subsequently, an LR or Golden gate reaction was set up with unpurified PCR product and befitting destination vector. We are able to construct expression clones within 36 h, which greatly improves efficiency and saves cost. Furthermore, the efficiency of this system was verified by an agrobacterium-mediated genetic transformation in rice. The system reported here provides a much more efficient and simpler procedure to construct expression clones for CRISPR/Cas9-mediated genome editing.

Rice Putative Methyltransferase Gene OsPMT16 Is Required for Pistil Development Involving Pectin Modification

Pectin synthesis and modification are vital for plant development, although the underlying mechanisms are still not well understood. Furthermore, reports on the function of pectin in the pistil are limited. Herein, we report the functional characterization of the OsPMT16 gene, which encodes a putative pectin methyltransferase (PMT) in rice. The cell walls of rice leaves contain less pectin, and chemical analysis of pectin in the flower organ had not been previously performed. Therefore, in the present study, the amount of pectin in the reproductive tissues of rice was investigated. Of the reproductive tissues, the pistil was especially rich in pectin; thus, we focused on the pistil. OsPMT16 expression was confirmed in the pistil, and effects of pectin methylesterification regulation on the reproductive stage were investigated by studying the phenotype of the T-DNA insertion mutant. The ospmt16 mutant showed significantly reduced fertility. When the flowers were observed, tissue morphogenesis was abnormal in the pistil. Immunofluorescence staining by pectin-specific monoclonal antibodies of the pistil revealed that total pectin and esterified pectin were decreased among ospmt16 mutants. These results indicate that OsPMT16 contributes significantly to pistil development during reproductive growth.

CRISPR/Cas9-Mediated Gene Editing of the Jasmonate Biosynthesis OsAOC Gene in Rice

The function of Jasmonate (JA) is well documented in different plant physiological processes as well as in the interactions with their environment. Mutants impaired in JA production and/or signaling are useful materials to study the function of this phytohormone. Genes involved in the JA biosynthesis pathway in rice have been described, but few mutants deficient in JA production and signaling have been identified. Moreover, these mutants are mostly generated through random mutagenesis approaches, such as irradiation, EMS treatment, or T-DNA insertion, and potentially harbor undesired mutations that could affect other biological processes. The CRISPR/Cas9 system is a precise and efficient genome editing tool that creates DNA modification at specific loci and limit undesired mutations.In this chapter, we describe a procedure to generate new JA-deficient mutant using CRISPR/Cas9 system in rice. The Allene Oxide Cyclase (OsAOC) gene is targeted since it is a single copy gene in the JA biosynthesis pathway in rice. The widely used variety Oryza sativa japonica Kitaake has been chosen due to its short life cycle and its ease of genetic transformation. This protocol describes the selection of the 20-nt target sequence, construction of the binary vector, and strategy for selecting the T-DNA-free mutant.

Comparative analysis of metabolome of rice seeds at three developmental stages using a recombinant inbred line population

Plants are considered an important food and nutrition source for humans. Despite advances in plant seed metabolomics, knowledge about the genetic and molecular bases of rice seed metabolomes at different developmental stages is still limited. Here, using Zhenshan 97 (ZS97) and Minghui 63 (MH63), we performed a widely targeted metabolic profiling in seeds during grain filling, mature seeds and germinating seeds. The diversity between MH63 and ZS97 was characterized in terms of the content of metabolites and the metabolic shifting across developmental stages. Taking advantage of the ultra-high-density genetic map of a population of 210 recombinant inbred lines (RILs) derived from a cross between ZS97 and MH63, we identified 4681 putative metabolic quantitative trait loci (mQTLs) in seeds across the three stages. Further analysis of the mQTLs for the codetected metabolites across the three stages revealed that the genetic regulation of metabolite accumulation was closely related to developmental stage. Using in silico analyses, we characterized 35 candidate genes responsible for 30 structurally identified or annotated compounds, among which LOC_Os07g04970 and LOC_Os06g03990 were identified to be responsible for feruloylserotonin and l-asparagine content variation across populations, respectively. Metabolite-agronomic trait association and colocation between mQTLs and phenotypic quantitative trait loci (pQTLs) revealed the complexity of the metabolite-agronomic trait relationship and the corresponding genetic basis.

Using natural variation to achieve a whole-plant functional understanding of the responses mediated by jasmonate signaling

The dramatic advances in our understanding of the molecular biology and biochemistry of jasmonate (JA) signaling have been the subject of several excellent recent reviews that have highlighted the phytohormonal function of this signaling pathway. Here, we focus on the responses mediated by JA signaling which have consequences for a plant's Darwinian fitness, i.e. the organism-level function of JA signaling. The most diverse module in the signaling cascade, the JAZ proteins, and their interactions with other proteins and transcription factors, allow this canonical signaling cascade to mediate a bewildering array of traits in different tissues at different times; the functional coherence of these diverse responses are best appreciated in an organismal/ecological context. From published work, it appears that jasmonates can function as the 'Swiss Army knife' of plant signaling, mediating many different biotic and abiotic stress and developmental responses that allow plants to contextualize their responses to their frequently changing local environments and optimize their fitness. We propose that a deeper analysis of the natural variation in both within-plant and within-population JA signaling components is a profitable means of attaining a coherent whole-plant functional perspective of this signaling cascade, and provide examples of this approach from the Nicotiana attenuata system.

The B-box zinc finger protein MdBBX20 integrates anthocyanin accumulation in response to ultraviolet radiation and low temperature

Ultraviolet-B (UV-B) radiation and low temperature promote the accumulation of anthocyanins, which give apple skins their red colour. Although many transcription regulators have been characterized in the UV-B and low-temperature pathways, their interregulation and synergistic effects are not well understood. Here, a B-box transcription factor gene, MdBBX20, was characterized in apple and identified to promote anthocyanin biosynthesis under UV-B conditions in field experiments and when overexpressed in transgenic apple calli. The transcript level of MdBBX20 was significantly induced by UV-B. Specific G-box elements in the promoters of target genes were identified as interaction sites for MdBBX20. Further experimental interrogation of the UV-B signalling pathways showed that MdBBX20 could interact with MdHY5 in vitro and in vivo and that this interaction was required to significantly enhance the promoter activity of MdMYB1. MdBBX20 also responded to low temperature (14°C) with the participation of MdbHLH3, which directly bound a low temperature-response cis elements in the MdBBX20 promoter. These findings demonstrate the molecular mechanism by which MdBBX20 integrates low-temperature- and UV-B-induced anthocyanin accumulation in apple skin.

Transcriptional Profile Corroborates that bml Mutant Plays likely Role in Premature Leaf Senescence of Rice (Oryza sativa L.)

Leaf senescence is the last period of leaf growth and a dynamic procedure associated with its death. The adaptability of the plants to changing environments occurs thanks to leaf senescence. Hence, transcriptional profiling is important to figure out the exact mechanisms of inducing leaf senescence in a particular crop, such as rice. From this perspective, leaf samples of two different rice genotypes, the brown midrib leaf (bml) mutant and its wild type (WT) were sampled for transcriptional profiling to identify differentially-expressed genes (DEGs). We identified 2670 DEGs, among which 1657 genes were up- and 1013 genes were down-regulated. These DEGs were enriched in binding and catalytic activity, followed by the single organism process and metabolic process through gene ontology (GO), while the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the DEGs were related to the plant hormone signal transduction and photosynthetic pathway enrichment. The expression pattern and the clustering of DEGs revealed that the WRKY and NAC family, as well as zinc finger transcription factors, had greater effects on early-senescence of leaf compared to other transcription factors. These findings will help to elucidate the precise functional role of bml rice mutant in the early-leaf senescence.

Metabolic GWAS-based dissection of genetic bases underlying the diversity of plant metabolism

Plants have served as sources providing humans with metabolites for food and nutrition, biomaterials for living, and treatment for pain and disease. Plants produce a huge array of metabolites, with an immense diversity at both the population and individual levels. Dissection of the genetic bases for metabolic diversity has attracted increasing research attention. The concept of genome-wide association study (GWAS) was extended to studies on the diversity of plant metabolome that benefitted from the development of mass-spectrometry-based analytical systems and genome sequencing technologies. Metabolic genome-wide association study (mGWAS) is one of the most powerful tools for global identification of genetic determinants for diversity of plant metabolism. Recently, mGWAS has been performed for various species with continuous improvements, providing deeper insights into the genetic bases of metabolic diversity. In this review, we discuss fully the achievements to date and remaining challenges that are associated with both mGWAS and mGWAS-based multi-dimensional analysis. We begin with a summary of GWAS and its development based on statistical methods and populations. As variation in targeted traits is essential for GWAS, we review metabolic diversity and its rise at both the population and individual levels. Subsequently, the application of mGWAS for plants and its corresponding achievements are fully discussed. We address the current knowledge on mGWAS-based multi-dimensional analysis and emerging insights into the diversity of metabolism.

Exploring the Diversity of Plant Metabolism

Plants produce a huge array of metabolites, far more than those produced by most other organisms. Unraveling this diversity and its underlying genetic variation has attracted increasing research attention. Post-genomic profiling platforms have enabled the marriage and mining of the enormous amount of phenotypic and genetic diversity. We review here achievements to date and challenges remaining that are associated with plant metabolic research using multi-omic strategies. We focus mainly on strategies adopted in investigating the diversity of plant metabolism and its underlying features. Recent advances in linking metabotypes with phenotypic and genotypic traits are also discussed. Taken together, we conclude that exploring the diversity of metabolism could provide new insights into plant evolution and domestication.

Characterization and subcellular localization of histone deacetylases and their roles in response to abiotic stresses in soybean

BACKGROUND

Histone deacetylases (HDACs) function as key epigenetic factors in repressing the expression of genes in multiple aspects of plant growth, development and plant response to abiotic or biotic stresses. To date, the molecular function of HDACs is well described in Arabidopsis thaliana, but no systematic analysis of this gene family in soybean (Glycine max) has been reported.

RESULTS

In this study, 28 HDAC genes from soybean genome were identified, which were asymmetrically distributed on 12 chromosomes. Phylogenetic analysis demonstrated that GmHDACs fall into three major groups previously named RPD3/HDA1, SIR2, and HD2. Subcellular localization analysis revealed that YFP-tagged GmSRT4, GmHDT2 and GmHDT4 were predominantly localized in the nucleus, whereas GmHDA6, GmHDA13, GmHDA14 and GmHDA16 were found in both the cytoplasm and nucleus. Real-time quantitative PCR showed that GmHDA6, GmHDA13, GmHDA14, GmHDA16 and GmHDT4 were broadly expressed across plant tissues, while GmHDA8, GmSRT2, GmSRT4 and GmHDT2 showed differential expression across various tissues. Interestingly, we measured differential changes in GmHDACs transcripts accumulation in response to several abiotic cues, indicating that these epigenetic modifiers could potentially be part of a dynamic transcriptional response to stress in soybean. Finally, we show that the levels of histone marks previously reported to be associated with plant HDACs are modulated by cold and heat in this legume.

CONCLUSION

We have identified and classified 28 HDAC genes in soybean. Our data provides insights into the evolution of the HDAC gene family and further support the hypothesis that these genes are important for the plant responses to environmental stress.

Modularity in Jasmonate Signaling for Multistress Resilience

The plant hormone jasmonate coordinates immune and growth responses to increase plant survival in unpredictable environments. The core jasmonate signaling pathway comprises several functional modules, including a repertoire of COI1-JAZ (CORONATINE INSENSITIVE1-JASMONATE-ZIM DOMAIN) coreceptors that couple jasmonoyl-l-isoleucine perception to the degradation of JAZ repressors, JAZ-interacting transcription factors that execute physiological responses, and multiple negative feedback loops to ensure timely termination of these responses. Here, we review the jasmonate signaling pathway with an emphasis on understanding how transcriptional responses are specific, tunable, and evolvable. We explore emerging evidence that JAZ proteins integrate multiple informational cues and mediate crosstalk by propagating changes in protein-protein interaction networks. We also discuss recent insights into the evolution of jasmonate signaling and highlight how plant-associated organisms manipulate the pathway to subvert host immunity. Finally, we consider how this mechanistic foundation can accelerate the rational design of jasmonate signaling for improving crop resilience and harnessing the wellspring of specialized plant metabolites.

Rice Functional Genomics Research: Past Decade and Future

Rice (Oryza sativa) is a major staple food crop for more than 3.5 billion people worldwide. Understanding the regulatory mechanisms of complex agronomic traits in rice is critical for global food security. Rice is also a model plant for genomics research of monocotyledons. Thanks to the rapid development of functional genomic technologies, over 2000 genes controlling important agronomic traits have been cloned, and their molecular biological mechanisms have also been partially characterized. Here, we briefly review the advances in rice functional genomics research during the past 10 years, including a summary of functional genomics platforms, genes and molecular regulatory networks that regulate important agronomic traits, and newly developed tools for gene identification. These achievements made in functional genomics research will greatly facilitate the development of green super rice. We also discuss future challenges and prospects of rice functional genomics research.

Genetic Dissection of Leaf Senescence in Rice

Leaf senescence, the final stage of leaf development, is a complex and highly regulated process that involves a series of coordinated actions at the cellular, tissue, organ, and organism levels under the control of a highly regulated genetic program. In the last decade, the use of mutants with different levels of leaf senescence phenotypes has led to the cloning and functional characterizations of a few genes, which has greatly improved the understanding of genetic mechanisms underlying leaf senescence. In this review, we summarize the recent achievements in the genetic mechanisms in rice leaf senescence.

Histone Deacetylase AtSRT1 Links Metabolic Flux and Stress Response in Arabidopsis

How plant metabolic flux alters gene expression to optimize plant growth and response to stress remains largely unclear. Here, we report that Arabidopsis thaliana NAD⁺-dependent histone deacetylase AtSRT1 negatively regulates plant tolerance to stress and glycolysis but stimulates mitochondrial respiration. We found that AtSRT1 interacts with Arabidopsis cMyc-Binding Protein 1 (AtMBP-1), a transcriptional repressor produced by alternative translation of the cytosolic glycolytic enolase gene LOS2/ENO2. We demonstrated that AtSRT1 could associate with the chromatin of AtMBP-1 targets LOS2/ENO2 and STZ/ZAT10, both of which encode key stress regulators, and reduce the H3K9ac levels at these genes to repress their transcription. Overexpression of both AtSRT1 and AtMBP-1 had synergistic effects on the expression of glycolytic genes, glycolytic enzymatic activities, and mitochondrial respiration. Furthermore, we found that AtMBP-1 is lysine-acetylated and vulnerable to proteasomal protein degradation, while AtSRT1 could remove its lysine acetylation and significantly enhance its stability in vivo. Taken together, these results indicate that AtSRT1 regulates primary metabolism and stress response by both epigenetic regulation and modulation of AtMBP-1 transcriptional activity in Arabidopsis.